7UCH

AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and Di-methyl-malonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6B3A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29311mg/mL protein in 50mM Tris pH7.4, 50mM NaCl, 10%(V/V) glycerol, 1mM S-adenosyl-L-homocysteine (SAH), and 5mM MnCl2. Well solution: 15% PEG 3350, 0.1M di-methyl-malonate Protein to well solution ratio is 2:2
Crystal Properties
Matthews coefficientSolvent content
2.4349.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.572α = 90
b = 88.283β = 90
c = 135.982γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1845.2399.870.9957.3710.63874933.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1812.25999.420.4951.18

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6B3A2.1845.231.3538749365699.870.19550.1930.241140.78
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.8011
f_angle_d0.8997
f_chiral_restr0.0522
f_bond_d0.0075
f_plane_restr0.0074
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5149
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms42

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction